"Model-based wavefront shaping microscopy"
Matlab scripts to generate all the data underlying the article "Model-based wavefront shaping microscopy" [ Correspondence to: a.thendiyammal@utwente.nl]
Comparison of Model-based wavefront shaping and feedback-based wavefront shaping
Running sequence:
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Generate refractive index map from TPM intensity images.
(a) Run /refractive_index_mapping/ShearTPMimage.m for coverting the acquired TPM frames to actual size in micrometer.
Input file: Image from ScanImage (Here, eg. PDMS_diffuser_surface_1X512.tif) Output file: TPM_3D.m(b) Run Refractive_Indexmap_3D.m to generate refractive index distribution.
Required input: TPM_3D from the previous step. Output file: Sample properties (eg. n_sample, PDMS_thickness) -
Run Model_WFS_PhaseConjugation.m for simulating light propagation through the PDMS diffuser to find correction wavefront.
Input: SampleProperties.m Output: SLMCorrection.m -
Run feedback_optimization.m for finding the optimal wavefront.
Output: ideal_wavefront.m -
Run WFScomparison.m for generating the Phase pattern on the SLM and compare the model-based wavefront shaping with feedback-based wavefront shaping.
Inputs: SLMCorrection and ideal_wavefront
Data Analysis codes:
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ModelWFS_DataStitching.m is used to stitch 3D substacks to form a combined 3D stack.
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ModelWFS_DataAnalysis.m - Generate maximum intensity projection. Compute mean intensity of the beads as a function of depth.
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plotSLMpatterns: Generate SLM patterns at different depths. Four patterns corresponding to four depths are used in the paper.